rs11022157

chr11-2301599-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001329958.2(C11orf21):c.53+157G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 631,506 control chromosomes in the GnomAD database, including 29,131 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.26 (6112 hom., cov: 32)
  • Exomes 𝑓: 0.30 (23019 hom.)
• Consequence: C11orf21 NM_001329958.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

Genes affected

C11orf21 (HGNC:13231): (chromosome 11 open reading frame 21) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C11orf21	NM_001329958.2	c.53+157G>T		intron_variant		ENST00000381153.8
C11orf21	NM_001142946.3	c.106+157G>T		intron_variant
C11orf21	NR_138249.2	n.259+1283G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C11orf21	ENST00000381153.8	c.53+157G>T		intron_variant		1	NM_001329958.2	A2
C11orf21	ENST00000456145.2	c.106+157G>T		intron_variant		1		P2
C11orf21	ENST00000470369.1	n.274G>T		non_coding_transcript_exon_variant	1/2	5
C11orf21	ENST00000495467.1	n.168+1283G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39973 AN: 151994 Hom.: 6113 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.305

GnomAD4 exome AF: 0.298 AC: 142992 AN: 479392 Hom.: 23019 Cov.: 6 AF XY: 0.298 AC XY: 73747 AN XY: 247684

Gnomad4 AFR exome AF: 0.109

Gnomad4 AMR exome AF: 0.217

Gnomad4 ASJ exome AF: 0.370

Gnomad4 EAS exome AF: 0.132

Gnomad4 SAS exome AF: 0.235

Gnomad4 FIN exome AF: 0.229

Gnomad4 NFE exome AF: 0.334

Gnomad4 OTH exome AF: 0.295

GnomAD4 genome AF: 0.263 AC: 39975 AN: 152114 Hom.: 6112 Cov.: 32 AF XY: 0.257 AC XY: 19095 AN XY: 74358

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.304

Alfa AF: 0.339 Hom.: 11656

Bravo AF: 0.260

Asia WGS AF: 0.216 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.3
Dann	Benign	0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11022157; hg19: chr11-2322829; COSMIC: COSV51719261; COSMIC: COSV51719261;